The human apurinic/apyrimidinic endonclease-1/redox factor-1 (APE1) protein is associated with the processing of abasic DNA sites via the base excision repair pathway and with the transcriptional activation of genes associated with redox regulation. The genetic deletion of APE1 is lethal both in vitro and in vivo, presumably as a result of the formation of the 10,000 abasic sites the form per cell per day. Accordingly, efforts have been made to develop small molecules that can inhibit APE1 activity in a controlled fashion. Such molecules will be useful tools to understand the multiple functions of the protein and how it interacts with other proteins and pathways. From a therapeutic standpoint, these small molecule inhibitors may be exploited to overcome the resistance of some tumor cells to DNA damaging agents that results from overexpression of base excision repair pathway proteins.
Prior attempts to generate small molecule inhibitors of APE1 have had some limited success. In one case, the results with indolecarboxamide based molecules have been difficult to reproduce. The inhibitory molecules are generally dicarboxylic acids or related analogs that mimic the (—O—PO2—O—R—O—PO2O—)—2 diphosphate substrate of the enzyme. In another study, the molecules, also dianionic, inhibitors based on arylstibinic acids, lacked activity in cells despite their excellent activity against the protein in a biochemical assay. In a third study, compounds from the Sigma-Aldrich Library of Pharmacologically Active Compounds (LOPAC) were screened and some active compounds identified. One compound that has been pursued is 7-nitro-1H-indole-2-carboxylic acid.
Although technically not an inhibitors of APE1 activity, methoxylamine (MeONH2) binds to the aldehyde in the ring-opened form of the AP site to yield a stable methoxyoxime derivative that cannot be processed by APE1. Accordingly, there have been attempts to clinically use MeONH2 in Phase I trials to enhance the cytoxicity of DNA damaging drugs that induce AP sites as repair intermediates.
In general, all prior attempts to generate inhibitors of APE1 have led to molecules with no activity in cells or low specificity.